# Optical Coherence Tomography (OCT) images

**URL:** <https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171>\
**Category:** VMTK\
**Tags:** oct\
**Created:** [October 20, 2020, 7:52pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171 "2020-10-20T19:52:02Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![syedf](https://avatars.discourse-cdn.com/v4/letter/s/7bcc69/32.png) [@syedf](https://discourse.slicer.org/u/syedf)\
**Post date:** [October 20, 2020, 7:52pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/1 "2020-10-20T19:52:02Z")

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Hello,

I was wondering if VMTK can segment OCT .dcm images. I’ve used VMTK before for MRI/CT dicoms, but when I try it for the OCT file, I get no output. The PypePad executes, but stops after a while.

Command:  
vmtklevelsetsegmentation -ifile Dicom/Patient\_02/IM-0001-0000-0001.dcm -ofile global.vti

PypePad:  
LevelSetsOutputFilename = global.vti  
FeatureImageOutputFilename =

and nothing after this.

The command prompt produces the following error:  
This application has requested the Runtime to terminate it in an unusual way.

Please let me know if there is any information regarding this.

Thanks!

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [October 20, 2020, 10:25pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/2 "2020-10-20T22:25:01Z")

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OCT images are typically much lower quality than CT and MRI, so it is not surprising if automatic segmentation fails, but you can try to apply some processing that makes them more similar to CT: convert RGB images to grayscale, apply noise filtering, vessel enhancement, etc. If you post a few example images then we might have more specific suggestions.

If automatic segmentation fails then you can always segment your image manually, using Segment Editor module in 3D Slicer.

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**Author:** ![shabnam\_esmaeelzadeh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shabnam_esmaeelzadeh/32/9090_2.png) [@shabnam\_esmaeelzadeh](https://discourse.slicer.org/u/shabnam_esmaeelzadeh)\
**Post date:** [December 5, 2020, 6:41pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/3 "2020-12-05T18:41:03Z")

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Hello  
How to insert a DICOM or radiology image into software such as simvascular?

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**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [December 5, 2020, 6:46pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/4 "2020-12-05T18:46:00Z")

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What would you like to achieve?  
Most software that works with medical images can read images from DICOM files.

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**Author:** ![shabnam\_esmaeelzadeh](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/shabnam_esmaeelzadeh/32/9090_2.png) [@shabnam\_esmaeelzadeh](https://discourse.slicer.org/u/shabnam_esmaeelzadeh)\
**Post date:** [December 6, 2020, 5:30pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/5 "2020-12-06T17:30:36Z")

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Thanks for the response, to build three-dimensional geometry of the aorta. From which site can I find DICOM photos?

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**Author:** ![guangxv](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/guangxv/32/9024_2.png) [@guangxv](https://discourse.slicer.org/u/guangxv)\
**Post date:** [December 7, 2020, 4:50pm UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/6 "2020-12-07T16:50:44Z")

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In my experiment, it is more easier to use ImageJ to segment OCT images semi-automiticly. ImageJ-\>Plugins-\>Segmentation Editor.

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<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [December 8, 2020, 2:23am UTC](https://discourse.slicer.org/t/optical-coherence-tomography-oct-images/14171/7 "2020-12-08T02:23:26Z")

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> [@shabnam\_esmaeelzadeh](#):
>
> Thanks for the response, to build three-dimensional geometry of the aorta. From which site can I find DICOM photos?

@shabnam_esmaeelzadeh Do you work with OCT data?

> [@guangxv](#):
>
> In my experiment, it is more easier to use ImageJ to segment OCT images semi-automiticly. ImageJ-\>Plugins-\>Segmentation Editor.

What kind to semi-automatic segmentation plugins ImageJ’s Segmentation Editor has? I’ve checked what is in Fiji-\>Plugins-\>Segmentation Editor and found this thing:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/5/d5683e57d017c2acd864daf853814cbbd24cd343.jpeg)

Do you mean that you would recommend this instead of Slicer’s Segment Editor? Have you tried the [Segment Editor module in Slicer](https://uide/image_segmentation.html#segment-editor-module)?

![](https://github.com/Slicer/Slicer/releases/download/docs-resources/image_segmentation_segment_editor_module.png)